I have a very large, merged BAM file which I successfully converted to a bedgraph using the "Create a BedGraph of genome coverage" tool. I was then trying to convert this file to bigwig format (to aid viewing with IGV) using the Wig/BedGraph-to-bigWig tool with the default settings. However, I get the following error:

Thanks for your comment. I admit it does look like that sort of problem, but I have only one genome file, which I have used for every step of the procedure, so there shouldn't be any chromosome name mismatches. The genome file has several hundred contigs that derive from two sources: first, the original JGI genome assembly and second, subsequent assemblies of reads not included in the JGI assembly. Hence the name format of the contigs is not consistent: some names are just digits, others have the form "contig_digits" and others "scaffold_digits". I wonder if this could be causing problem? I provide a link to a "genome.txt" file which lists the "chromosomes" and their sizes, so you can see what I mean:

I don't think the contig names in the genome,txt file are cusing troubles. I am actually more concerned about the total number of "chromosomes" you have: 12744 How do you wanna a look at those in IGV (or Galaxy trackster)?

Maybe it will help filter the bam file to those contigs you are actually intersted in?

So you think the large number of "chromosomes" is causing trouble for the bedgraph-to-bigwig tool? I don't think it's critical that it's in bigWig format, so maybe I'll give up.

This is the world of non-model organisms with rather imperfect genome assemblies.I'm really an experimentallist, trying to create a resource for myself and others in my group. We do lots of proteomic experiments which identify proteins and genes that are potentially involved in our process of interest. When we identify such a GOI we need to be able to assess the evidence for the gene models at that locus such that we can plan subsequent experiments. Thus I'm mapping the available gene models from the JGI predictions to our improved genome, as well as all available RNAseq data. For the latter I was summarizing the results in a single bedgraph. I can view this perfectly well for a locus of interest in the IGB, and I've made a quickload site for everyone in our group to access, but I wanted to explore what IGV has to offer as well.

not yet, but I should give it a go - I'm much more comfortable in linux than I was two weeks ago - much thanks to all the professional bioinfomaticians on sites like this that give their time to answer my questions!